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OK,I don't have the code list in front of me.If what you say is true then look for loose wiring in both the line and low voltage wiring.
If you have junction boxes between the breaker panel and the unit,then run a single line stright from breaker panel to the unit.Also make sure thebare wire is properly attached to the panel and to the furnace and the white and black wires are correct in the panel and where it attaches to the module in the furnace.With a meter check the line voltage for 120v.
With a meter check the transformer output.
You really need full power because when voltage gets to the flame sensor its so small that a minor drop in the supply will affect the sensor voltage.